Mass Effect Through the darkness
by jamie1907
Summary: An alternative ME3 featuring FemShep Miranda romance. As the threat of the reaper grow, the races of the galaxy are left with only one choice stand together or die alone.
1. Chapter 1

Mass effect through the darkness (An alternative ME3) Focusing mainly on shepherd and Miranda but will have the bulk of character from ME1 and ME2. Written by someone completely disappointed by ME3. Am writing a slightly altered version of ME2 that will explain back story.

Prelog.

Commander Elena shepherd was jolted awake by a noise in the distance. She glanced up at the window to see the sun setting. She stood up to look over the city stretching out in front of her. She been born on a ship that bore the city name but the SSV Manchester had long scraped.

Both her parents had been born on the Island, thus shepherd faint British accent. She stood there for a long monument before returning to the couch. She been here for six months just waiting, the alliance parliament was dragging its heels on what to do, so other than being charged nothing had happened.

She glanced down at the copper ring on her finger and her thoughts turned to Miranda. She had not seen her since she handed back the Normandy over to alliance force. She had no idea where the former Cerberus was but hoped she be busy, trying to find so way to stop the reapers. Suddenly there was a beeping from the intercom. She made her way over and pushed the receive button.

''Shepherd you've lawyer is here to see you.''

Shepherd was confused, she had a vague reference of being told who her lawyer was but had never actual met them.

''Well I'm not going anywhere.''

Shepherd retuned to couch and picked up the book she been reading. It was five minutes before she heard the noise of the door opening. She glanced up to see a woman entering accompanied by a marine. The woman step forward, she was wearing a suit jacket over a light blue shirt accompanied by a very short skirt.

''Hello Miss Shepherd I'm Hanna Gray...''

Shepherd blinked, the woman had blond hair and glasses but behind that it was.

''Miria...''

The woman shot her a look than turned to the guard.

''Unless you plan to Miss the game I'd head back down, I'll call when we done.''

The guard, who already look disgruntled, turned and exited the room. Shepherd attempt to speak but the woman held up a hand. She waited until the door had closed and the sound of the elevator had faded.

''They really know how to pick them, don't they shepherd.''

The woman grasped her hair and pulled it off to relive the black hair below it.

''Mindi how on...''

Miranda tossed the wig on to a table and took of the glasses.

''Funny what you can do with a little appearance change.''

They both stood there for a monument, staring at the woman they agreed to marry. Shepherd spoke first.

''Missed me.''

''Night were the worst, I almost miss sneaking up to your quarters.''

There was silence.

''Elen...''

Miranda didn't get to finish as shepherd pined her to the wall. Their lips locked as they began making up for lost time.

Shepherd laid back on the bed, the sun had now set beyond the horizon filling the bed room with only the glow of the city light. She turned to see Miranda lying beside her.

''Satisfied Miss Lawson.''

Miranda turned to look at her.

''Very.''

Miranda took shepherd hand and pulled her in close.

'' Well how have you, been Elena?''

Shepherd smiled.

''The last few hours have been great, the rest...''

Shepherd trailed off.

''Told you.''

Shepherd shot her a look.

''I'm starting to think your right ... how are things out there.''

''I've kept busy, the shadow broker given me a few leads.''

''and Cerberus.''

''I've heard nothing since I quit.''

Shepherd kissed her on the fore head.

''Just be careful.''

''Always am.''

''Says the woman who pulled a Clark Kent, to see her girlfriend.''

'' fiancée commander.''

Shepherd smiled. Miranda glanced over at the clock.

''I'd better go, the guard may not be the smartest but they realise something up.''

Miranda stood up and began pulling on her clothes. Shepherd wanted her to stay but knew it was impossible so said nothing. She glanced at the stars, somewhere out there the reapers were slowly moving towards them and at the monument no one was doing anything.

''Elena.''

Miranda climbed back on to the bed and handed her a pendent. She opened it to reveal a picture of them. It was of them curled up on the couch in shepherd quarter on the Normandy two.

''When did you, take this?''

''You were pretty much asleep.''

Shepherd grinned and then placed the pendent over her neck. Miranda exited back into the main room, shepherd pulled on dressing gown and followed her out.

''Promise me you be careful.''

Miranda pulled on the wig and then turned to shepherd.

''Elena stop worrying, anyway I want that beach house ''

They hugged each other and then Miranda hit the intercom. They said nothing as they waited for the guard to arrive. It was only when the door opened, that they said anything.

''See you around commander.''

Shepherd said nothing as the door closed, leaving her alone again. She moved over to the window and stared out at the stars.

At the same time someone ell was staring out at them. Major Agustin De La Hoz turned to the men and women sitting in the vehicle behind him, who all wore the uniforms of the alliance army.

''Anyone who wants out this is your last chance.''

There was silence.

''Good luck everyone.''

They burst out onto the street and cover the distance to their target. As they may their way through the building, people scatted in front of them, Agustin mad his way to the target. By even being here he knew he was committing treason but he couldn't just sit back and do nothing. On finding his target he kicked the door in.

''What is the meaning of this?''

He turned to see the man he was after, he aimed a pistol at him.

''Tell me minister, how much did they buy you for?''

''What... this is treason.''

Agustin moved closer and grabbed the alliance parliament member by the collar.

''I know you work for Cerberus.''

Part one will hopeful be up soon.

Comment and reviews welcome

Please excuse any spelling and punctuation mistakes.

Thank you for reading.


	2. Chapter 2

Army of Albion.

Shepard was awoken by beeping from the intercom. She left it for a monument but the beeping continued. Grudgingly she climbed out of bed and over to the intercom.

''What?''

''Get dressed you got a visitor.''

Shepard glanced over at the clock. Three o'clock AM.

''Do you know what time it is?''

''Five minutes Sheppard, make sure it decent.''

The intercom went dead, Shepard turned and located the clothes she worn at the hearing yesterday. The situation had been made worst with the violence in Madrid; twelve Spanish army officers had seized the Spanish parliament building and arrested the Spanish representative on charges of treason. Alliance army units had surrounded the building but refused to storm it. The political situation was again split and poised on a knife edge.

She changed and then exited the room. To her surprise she found the door open and the elevator sitting open.

She entered it and was soon being whisked down toward the ground floor. It came to a stop well short of the ground floor and Shepard was greeted by a corridor she hadn't been in before. A man stood waiting for her.

''This way please Miss.''

The man was dressed in a suit, there was a emblem over the left breast but he had turned and moved off before Shepard got a closer look.

''Right a few ground rules. One speak only when spoken to, don't curtsey it drives him mad, call him your highness and finial don't mention his cousins are we clear.''

They arrived at a door two soldiers were standing ever side of it. They both wore dress uniform of scarlet one emblazed with the Cross of Saint Andrew, the other the red dragon of Wales. Shepard blinked.

''Wait, who, do you mean?''

''Yes Madam your about to meet a king.''

The doors opened to revile an office with a man standing, staring out at the city. On hearing the noise he turned. Shepard was greeted by the face of King Edward the XVIII (eighteen). She went to curtsey but stop before she finished.

''Miss Shepard I presume?''

The voice was not what she had expected, a real down to earth voice which all most didn't want to be heard.

''You're...''

He cut her off.

''Please none of that, if anyone in this room deserves respect it you.''

He degusted for her to sit and waited for her to take a seat before sitting down.

''Tell me Shepard... did you ever ...did you ever want this?''

''Want... What sir?''

There was silence for a monument.

''You're a hero Shepard, I mean some people see you as the second coming.''

''I never asked to be a hero sir.''

There was silence for a monument.

''Well then we both didn't ask for this.''

Edward stood up and looked out the window.

''I know there out there shepherd, the reapers I mean, most of the alliance brass does... but the other, they just hope it will just go away.''

'' Can't you do something sir?''

Edward laugh.

''Maybe a hundred years ago, I could have done something but today no.''

''Then why are you here sir.''

Edward turned to look at her.

''I may have found something, something that could help with the reaper problem.''

Shepard sat up.

''What...have you ...''

''Yes I informed the military, it was laughed off.''

Shepard sat back; she was beginning to think Edward was wasting her time, suddenly she hared a slam as a huge file was dropped on the table.

''Surprisingly Shepard my life is rather boring, giving me plenty of time to read... ''

Shepard began flicking threw the file; it contained pictures of what appeared to be ancient artwork but with what appeared to be reapers.

'' I found theses just sitting in museum across the world, I first I thought it was coincidence but then I looked at the data recover from the beacon on mars. There was what appeared to be a map which combined with several of theses. ''

Shepard flicked over to see a partial map pasted over several of the art work, a match.

''That map when laid over earth, point to south east England, I then thought I reached a brick wall but then I found this report.''

The file suddenly turned to a report. The bulk of it was blacked out but enough was visible to make sense what the report was about.

''In 1942 the British found something down a mine shaft in Kent; it scared them enough to seal the mine and collapse the shaft. ''

Shepard turned the page and was shocked with what see saw. A grimy black and white photo showed a crocodilian life form, clad in power armour slump against a wall, on the wall was another image showing a reaper being destroyed by some huge cannon. Shepard stood up.

''Sir we need to find this. ''

Edward look surprised but delighted at the same time.

''If only the alliance top brass, were that easily persuaded.''

Edward stood up.

''Well then Shepard If we leave now we should be there in an hour.''

It was only much later that Shepard realized how many rules she was breaking but by then there were far bigger problems.

Kent

Shepard glanced out the window of the shuttle. It had started raining obscuring the ground below. However there was enough activity on the ground to stand out. Edward hadn't stop talking since they left explaining on how he found every detail of his information. Shepard was surprised that the alliance hadn't even given him a token response, especially with Anderson as councillor. There was a bump as the shuttle landed. The door opened and a figure was standing there, glad in a green khaki military uniform. Shepard recognised it as the uniform of the alliance army. The star on his shoulder indicted the rank of major general.

''Well Eddy clad you could join us.''

The thick Scottish accent cut through the air and caused Shepard to jump. The figure glanced over to her.

''Well the great Shepard has chosen to join us.''

A flash of lighting broke across the sky, illuminating the figure face. Shepard recognised it almost instantly. It was General James Thomas Campbell, hero of the alliance and the only man who emerged from Shanxi with any honour.

When General William surrender the garrison, Campbell just a lowly company commander in the black watch had uttered a phrase not suitable for polite conversation and the basically went rogue with over a company of the black watch. The turian were unable to use their fleet fire power due to the fact the mining tunnel and sewers that covered the northern part of the colony provided natural cover for Campbell troops.

The turian's sent to flush them out came to call them demons due the ferocity they fought with and the bagpipes which drove them mad. By the time alliance relief force arrived there were only 14 able to answer the call to arms. The alliance made Campbell and his surviving troops the hero's of Shanxi and the black watch added Shanxi to its battle standard. Campbell response was simple ''for two hundred year this regiment has never surrender, I wasn't about to let those men down.''

'' don't tell me your worried about a little competition Campbell.''

Edward stood up and exited into the pouring rain. Campbell stood staring at Shepard for a second before turning and following Edward. Shepard had to sprint to catch up with them despite them both being at least 20 years older than her.

''We breeched the old mine yesterday, look like they went back at some point during the cold war, there a control room been dug into the side of the old shaft, we've set up shop there. There then a 50 foot drop down to the location where the brit's found the croc, were still to send a team down there.''

'' Well let just send a team down.''

Campbell turned to look at her.

''Shepard this place has had several cave in, we barely finished adding supports to the enter passage.

'' well then let me go, the reapers are coming and there may be a solution under our feet. ''

Campbell stood for a monument.

''Fine get yourself suited up, there should be something in the supplies.''

Campbell opened his omni-tool.

''Douglas get your squad suited up, you're going in.''

''Aye sir.''

Campbell gestured toward a group building. Shepard turned and jog over to the largest building. The door hissed open and she stepped in. A group of soldiers stood round a television screen, one turned on hearing the door open.

''Commander Shepard.''

On hearing her name they all turned round and snapped to attention.

''Ma'am, what are you doing here?''

''Campbell told me to suit up.''

One of them step forward.

''If you would follow me then Ma'am. ''

Shepard followed him threw corridor of the building; it had clearly been the control building for the mine and had clearly seen better days. They were passed by a group of soldiers kitted out with climbing equipment, probably the squad Campbell had called. They entered a room being used as an armoury.

''May I have your measurement Ma'am.''

Shepard opened her omni tool and send over her specs. The solider moved off along the shelves of equipment. He began pulling items of shelves, before turning back to Shepard.

''I must say, Ma'am your bigger in real life, the ads had you more like a stick insect.''

''Thank, I think.''

The equipment was placed in front of her.

''No N7 stuff Ma'am, just standard issue.''

''No problem.''

He handed over a pad, which Shepard signed.

''You can change in there Ma'am.''

He gestured to a room of to the side. Shepard entered and then closed the door. She stood there for a monument, she should have been thinking about what was going on but her thought were on one person.

''Be safe Miri.''

Outer alliance space New Washington

Miranda step out of the car and made her way toward the house. Jacob had contacted her a few days ago saying he found something. She made her way up to the house he sent as a place to meet. She found the door open and entered.

''Jacob.''

There was silence causing her to draw the pistol from her waist. She moved through the house, despite it outside look the house was run down and covered in cobwebs. She emerged in a dining room with an old table and chairs.

''Miranda.''

She turned to see Jacob sitting in the chair at the end of the table. On seeing him she lowered the pistol.

''Jacob what are we doing here, what with all the clock and dagger? ''

''I been told to bring you back.''

Suddenly she heard a noise, this was a trap. She felt something pierce her leg and her vision began to go blurry. She glanced down to see a dart emerging from her leg. She fell to the ground as the world began to go black but voices were still audible.

''Tell the Illusive man we collected the target. ''

In the growing darkness Miranda could only see pairs of blue eyes staring back at her. The world of sound and images both vanished and Miranda was alone in the darkness.

Codex entries

King Edward XVIII (eighteen).

Never has there been a more unlikely Monarch. Born 8th of March 2154 Edward wincer was fifteenth in line to the throne of Great Britain, Edward was deemed an almost no essential and was allowed to join the alliance military at the age of eighteen. Choosing the alliance medical service Edward had risen to the rank of medical officer Edward life seemed destined for normality until the event's of the 13 November 2176. A bomb placed inside Buckingham place during the Prince of Wales birthday celebrations explode, killing the royal family as well as over a hundred others. Edward was stationed with alliance 5th army on desert exercises and avoided the events, after a week it had become clear that he was now king. Edward was crowned Edward the eighteenth a month later.

General James Thomas Campbell.

Born in Orkney 2137 James Thomas Campbell rose quickly within the rank of the alliance army but it was during the battle of Shanxi where he came to the spotlight. Fighting a fanatical defence against superior Turian forces, Campbell and his troops held out until the alliance counter attack swept the Turians form the planet. He has since risen to the rank of general and appointed as head of northern command, earth defence force.

Thanks for reading and hope you enjoyed.


	3. Chapter 3

Shepard stood on the edge of the precipice; there were faint glimmer of light, from the beacon already lowered into the pit.

''It's a fifty foot drop down to the other shaft, that where they claimed to find the body.''

Campbell stood away from the edge addressing the group preparing to descend.

''I know you take orders from Douglas but this time you take orders from Shepard. ''

There was a mummer.

''No problem sir.''

The solider next to Shepard turned to him.

''You saved my life, on the citadel Shepard; I've got your back. ''

Shepard smiled beneath her helmet.

''Thanks.''

Shepard took a step back and let the rope take her weight. She began repelling down the side of the shaft her boots making imprints in the side of the pit. Slowly the lights of enters passage began to fade. Shepard suddenly heard something, as if someone was talking in the distance.

''Sorry say again.''

''No one said anything Shepard.''

The noise stopped, leaving nothing but the tunnel. Suddenly the bottom of the pit appeared out of the darkness. Shepard lowered herself the last couple of feet and dropped to the floor. She looked down the tunnel the first person for a least a century.

''I'm at the floor.''

Her torch beam lit up the dark passage. She saw a faint glimmer of something bone white at the end of the passage. Suddenly the noise was back as if someone was talking next to her, she spun round only to see the rest of the soldiers just stepping of the rim of the shaft. The noise vanished again, leaving the dank silence of the pit.

The hours passed.

Madrid

Agustin was jolted awake as the sound of shuttle appeared over head. He made his way over to the window. The shuttles began touching down on the other side of the police perimeter.

''anybody got an I.D?''

''presidential guard sir.''

Agustin picked up his assault rifle.

''So Look like Hudson, send in the goon squad.''

A click rang out as safeties were turned off. Agustin crouched down behind the window. He glanced down the scope; the guard were forming up on the other side of the perimeter. The crowd on the side street emerged from tents and other temporary structures, a wave of hissing and catcalls rang out as the guard formed a line on the edge of the square.

''Sir his eye are glowing.''

Agustin raised an eyebrow.

''Have you been drinking?''

''No sir, middle row in the third platoon.''

Agustin scanned the ranks of guardsmen, they all had there helmet's on with visors down but on one of them a crack ran along the visors. A blue light emerged from beneath the metal a light Agustin had seen before coming from those husk on Eden prime.

No one was ever sure of what happened next. A shot rang out from across square catching the guardsmen in the face smashing the visor; he spun round as a camera drone moved in, the face which was revelled was soon broadcast across the whole alliance a face worn down to the skull with nothing but the staring blue eyes.

It was then the shooting started.

Kent

Shepard slumped against the wall; they'd been down there for a few hours now but to no avail. Her thought turned to Miranda.

''Elena.''

Miranda voice rang softly around the shaft, nobody ells seemed to hear anything. Shepard turned half excepting to see Miranda standing next to her. She found she was facing the caved-in side of the shaft but it seemed odd. She made her way over to stare at the rock face, the rest of the shaft was covered with a thin slime but this rock face was completely dry.

''Shepard.''

Douglas appeared behind her.

''Why are these dry, whilst all the rest is damp?''

''I'll get one of the egg head to take a look.''

Shepard placed a hand on the rock, it felt solid but something still felt wrong. Suddenly the noise returned not a whisper but a yell. Suddenly the cave was gone replaced only by darkness.

''Shepard ... Shepard.''

Douglas looked around, Shepard had vanished.

Edward was awoken by the sound of Campbell yelling down the radio.

''What do you mean she Vanished?''

There was a muffled reply down the radio.

''Well find her''.

Campbell deactivated the radio and turned to Edward.

''Shepard Vanished.''

''Vanished.''

''Into thin air.''

Both men stared at each other. They were brought back to life by a radio operator.

''Sir there fighting in Madrid.''

''What?''

''Report coming in of Police and Army fighting the presidential guard, sir there report...''

Silence filled the control room.

''... there reports the guards are indoctrinated.''

The sound of a pen hitting the floor and the faint hum of computers was the only thing heard in the room. The silence continued before Edward's voice broke it.

''If the guards indoctrinated ...''

Campbell finished Edwards's sentence.

''then they could have the president.''

Suddenly there was a beep on the radar.

''Sir there a shuttle inbound, redcaps''

Campbell swore before turning out of the control room, for the monument Shepard was on her own.

Shepard body ache. It was as if all the scars healed during Lazarus had suddenly ripped open. She tried to move her arm but nothing happened other than another burst of pain, she stop trying to move and tried to take in her surroundings. There was nothing no sound, no light just nothing.

Suddenly voice filled her head; voices from her childhood all the way up to Campbell and Edward voices, all merging into one almost unbearable noise. Images began to fill her mind, her first kiss, her father funeral, join the marines, N7 training, sovereign, the destruction of the Normandy and then the collector base.

''has the committee come to a decision.''

A voice broke through the madness of swirling images and noise but then they were gone and sudden there was bright light. The sound of waves lasing against the shore, she was lying on a beach with the warmth of the sun lashing against her face. She moved her hand across her face to find the skin completely fine; her armour was gone replaced by a dark blue bikini.

''Elena.''

She turned to see Miranda sitting in a hammock slung between two palm trees.

''Mindi where is this?''

Miranda smiled.

''Just sit here please.''

She placed a hand on the hammock. For some reason all of Shepard problems vanished. She made her way over to the hammock and slid in next to Miranda, she felt an arm being placed around her and being pulled close.

''It will be ok Shepard.''

''Enough of this.''

The voice was back and this time it had a face, two yellow eyes staring at her. The beach was gone replaced again by the darkness, she was back wearing her armour but now she was in a swamp with foul smelling liquid bubbling up from a pool. Stone chair ringed it; each had a hole in the back a scaled tails emerged from them.

''We are agreed it not indoctrinated.''

A voice different from the first one emerged from one of the chair. She took a few steps forward; the creatures sitting in the chair looked like the one in the mine shaft, Scaled crocodilians with webbed arms that reached down to grasp the arms of the chairs. They ranged in colours from brown to dark green some had red scales dotted across their faces but with perusing yellow eyes staring across the low light.

''yes but the fact it down here is a big enough problem. ''

''The next cycle is nearly upon us, we should hid like we always done.''

''We won't survive another cycle, we lose members every day.''

''Do you believe theses warm blood can stop them?''

''Why don't we let it speak.''

Several pairs of eyes turned to her, she moved forward into the centre of the circle.

''Who...what are you?''

''We are the comity, Commander Shepard.''

''How do you, know my name?''

''We know everything.''

''We are thought walkers, we know and hear all.''

''Then you know why I'm here?''

''Yes you seek a super weapon do defeat the machines you call reapers, you will find none here.''

''but the...''

''Propaganda.''

Shepard turned round; the faces staring back at her seemed to look straight threw her, all except one.

''Do you think you can win?''

Shepard starred straight back at the creature that had just spoken; it was different from the others a scare ran the length of it face, It eyes looked dull but still burnt with the fire of a warrior.

''I don't know?''

A torrent of voices irrupted but was silenced by the creature with the scared raised it hand.

''Would you, die for her?''

The image of the first time she seen Miranda, that faint drug filled hallucination crept into Shepard head.

''Yes.''

Silence filled the room. The creature stared at Shepard before standing up.

''The warrior, votes to awaken, call the vote.''

The room vanished replaced with emptiness but suddenly light broke through. Shepard was lying on a table in what appeared to be a medical room. Something was moving off to one side. Suddenly a hiss broke the stillness and a pod emerged from the wall. She felt something on the back of her head, she tried to stand up but found one of her hands tied to the table. The pod opened to revile one of the crocodilians emerged. It stared at her for a monument before falling to its knees. The clasp on Shepard arm opened she stood up and was surprised to find her pistol still in it holster. She drew it and aimed it at the creature.

''right what the...''

''Red vile.''

Shepard looked puzzled before noticing a red vile on the table she been tied to. She moved over being careful to keep the gun aimed at the creature. She picked it up and then rolled it over to the creature. It picked up the vile and slid into a segment of it armour. It pulled itself up and leaned against the wall.

''Right who are you what is going on?''

''My name is Zanta am a solider of the Ival and we must act soon commander or the reapers will take your world without a shot being fired.''

Thank for reading.

All mass effect character property of bioware.


End file.
